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SNARE-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Profilin-like [ 55769] (10)
Superfamily:   SNARE-like [ 64356] (4)
Families:   Synatpobrevin N-terminal domain [ 64357] (2)
  Sedlin (SEDL) [ 82767]
  Clathrin coat assembly domain [ 75521] (2)
  SRP alpha N-terminal domain-like [ 90019] (2)


Superfamily statistics
Genomes (507) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 12,025 27,327 11
Proteins 11,964 27,217 11


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation11Least InformativeInherited
Biological Process (BP)cellular localization0.00000071290Moderately InformativeDirect
Biological Process (BP)nitrogen compound transport0.63580.0754Moderately InformativeInherited
Biological Process (BP)organic substance transport10.8118Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.061210.007887Moderately InformativeInherited
Biological Process (BP)regulation of localization0.45650.3914Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.83441Moderately InformativeInherited
Biological Process (BP)protein transport0.000000000010740InformativeDirect
Biological Process (BP)vesicle-mediated transport0.000000000013270InformativeDirect
Biological Process (BP)intracellular transport0.0000000039140InformativeDirect
Biological Process (BP)organelle localization10.8265InformativeInherited
Biological Process (BP)Golgi vesicle transport0.0000016710Highly InformativeDirect
Biological Process (BP)regulation of lipid localization0.00026050.00004991Highly InformativeDirect
Molecular Function (MF)binding0.64221Least InformativeInherited
Molecular Function (MF)transporter activity0.023390.04724Moderately InformativeInherited
Molecular Function (MF)molecular function regulator0.037370.156Moderately InformativeInherited
Molecular Function (MF)protein transporter activity0.000000000086330.00000000000001901Highly InformativeDirect
Molecular Function (MF)guanyl-nucleotide exchange factor activity0.00000066240.000004248Highly InformativeDirect
Cellular Component (CC)protein complex00Least InformativeDirect
Cellular Component (CC)membrane0.00000053810Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.082280.000000000000003036Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.048860.01105Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.0078970.00004363Least InformativeInherited
Cellular Component (CC)whole membrane00Moderately InformativeDirect
Cellular Component (CC)bounding membrane of organelle00Moderately InformativeDirect
Cellular Component (CC)endomembrane system0.000000000000053810Moderately InformativeDirect
Cellular Component (CC)membrane protein complex0.000000000028370Moderately InformativeDirect
Cellular Component (CC)vesicle0.000000011090Moderately InformativeDirect
Cellular Component (CC)plasma membrane0.99880.9733Moderately InformativeInherited
Cellular Component (CC)Golgi apparatus00InformativeDirect
Cellular Component (CC)cytoplasmic vesicle part00InformativeDirect
Cellular Component (CC)endosome0.57040.09734InformativeInherited
Cellular Component (CC)membrane region0.00030270.01389InformativeInherited
Cellular Component (CC)plasma membrane protein complex0.042250.2867InformativeInherited
Cellular Component (CC)membrane coat00Highly InformativeDirect
Cellular Component (CC)coated vesicle00Highly InformativeDirect
Cellular Component (CC)Golgi-associated vesicle0.000000000000016510Highly InformativeDirect
Cellular Component (CC)tethering complex0.000000000031580Highly InformativeDirect
Cellular Component (CC)cytoplasmic vesicle membrane0.0000014840.000007649Highly InformativeDirect
Cellular Component (CC)endocytic vesicle0.63790.07513Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular component organization or biogenesis 0.1034 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.007887 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.0754 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8118 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.3914 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.01433 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3461 Moderately Informative Inherited
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) intracellular transport 0 Informative Direct
Biological Process (BP) secretion by cell 0.0000000001516 Informative Direct
Biological Process (BP) single-organism membrane organization 0.0000001063 Informative Direct
Biological Process (BP) microtubule-based process 0.0000557 Informative Direct
Biological Process (BP) single-organism cellular localization 0.7848 Informative Inherited
Biological Process (BP) cell activation 0.01384 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.02527 Informative Inherited
Biological Process (BP) organelle localization 0.8265 Informative Inherited
Biological Process (BP) immune effector process 0.007311 Informative Inherited
Biological Process (BP) immune response 0.06694 Informative Inherited
Biological Process (BP) Golgi vesicle transport 0 Highly Informative Direct
Biological Process (BP) regulation of lipid localization 0.00004991 Highly Informative Direct
Biological Process (BP) phagocytosis 0.0007582 Highly Informative Direct
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) organelle fusion 0 Highly Informative Direct
Biological Process (BP) single-organism membrane fusion 0.00000000001182 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0000000008698 Highly Informative Direct
Biological Process (BP) neutrophil mediated immunity 0.0000005858 Highly Informative Direct
Biological Process (BP) granulocyte activation 0.0000008458 Highly Informative Direct
Biological Process (BP) leukocyte degranulation 0.00000112 Highly Informative Direct
Biological Process (BP) myeloid cell activation involved in immune response 0.000001998 Highly Informative Direct
Biological Process (BP) establishment of organelle localization 0.003842 Highly Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0.04724 Moderately Informative Inherited
Molecular Function (MF) molecular function regulator 0.156 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.002626 Informative Inherited
Molecular Function (MF) protein transporter activity 0.00000000000001901 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.000004248 Highly Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00004363 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000000000003036 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.01105 Least Informative Inherited
Cellular Component (CC) whole membrane 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) vacuole 0.0000005189 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.9733 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0 Informative Direct
Cellular Component (CC) vacuolar part 0.00000003434 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.00001808 Informative Direct
Cellular Component (CC) endosome 0.09734 Informative Inherited
Cellular Component (CC) membrane region 0.01389 Informative Inherited
Cellular Component (CC) plasma membrane protein complex 0.2867 Informative Inherited
Cellular Component (CC) lytic vacuole 0.02184 Informative Inherited
Cellular Component (CC) membrane coat 0 Highly Informative Direct
Cellular Component (CC) coated vesicle 0 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0 Highly Informative Direct
Cellular Component (CC) tethering complex 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.000007649 Highly Informative Direct
Cellular Component (CC) SNARE complex 0 Highly Informative Direct
Cellular Component (CC) lysosomal membrane 0.00002631 Highly Informative Direct
Cellular Component (CC) endoplasmic reticulum-Golgi intermediate compartment 0.00002916 Highly Informative Direct
Cellular Component (CC) endocytic vesicle 0.07513 Highly Informative Inherited
Cellular Component (CC) late endosome 0.1636 Highly Informative Inherited
Cellular Component (CC) endosome membrane 0.828 Highly Informative Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Biological processExocytosis0.0000001697Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCell junction0.003082Moderately InformativeInherited
Cellular componentLysosome0.0000008258InformativeDirect
Cellular componentSynapse0.000003222InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Cellular componentSynaptosome0.00000927Highly InformativeDirect
DomainTransmembrane0.000002847Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionLipid-binding0.000001835Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.000001917Least InformativeDirect
Post-translational modificationAcetylation0.000005068Least InformativeDirect
Post-translational modificationPalmitate0.0000000000001606Moderately InformativeDirect
Post-translational modificationMethylation0.000001015Moderately InformativeDirect
Post-translational modificationPrenylation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011012 SSF64356 Protein matches
Abstract

VAMPs (and its homologue synaptobrevins) define a group of SNARE proteins that contain a C-terminal coiled-coil/SNARE motif, in combination with variable N-terminal domains that are used to classify VAMPs: those containing longin N-terminal domains (~150 aa) are referred to as longins, while those with shorter N-termini are referred to as brevins [PubMed12914952]. Longins are the only type of VAMP protein found in all eukaryotes, suggesting that their longin domain is essential. The longin domain is thought to exert a regulatory function. Longin domains have been shown to share the same structural fold, a profilin-like globular domain consisting of a five-stranded antiparallel beta-sheet that is sandwiched by an alpha-helix on one side, and two alpha-helices on the other (beta(2)-alpha-beta(3)-alpha(2)).

Other families have been shown to contain domains that structurally resemble the VAMP longin domain. An example is the eukaryotic conserved protein, SEDL, which is a component of the transport protein particle (TRAPP), critically involved in endoplasmic reticulum-to-Golgi vesicle transport; mutations in the SEDL gene are associated with an X-linked skeletal disorder, spondyloepiphyseal dysplasia tarda [PubMed12361953]. Another example is the assembly domain of clathrin coat proteins, such as Mu2 adaptin (AP50) and Sigma2 adaptin (AP17), which structurally resemble the longin domain. AP50 and AP17 are two of the proteins that make up the core of AP2, a complex that functions in clathrin-mediated endocytosis [PubMed12086608].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 7 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a SNARE-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 7 hidden Markov models representing the SNARE-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]